Integrating Morphology and Chloroplast Genomics: A New East Asian Species of <i>Aletris</i> (Nartheciaceae) With Insights Into Regional Phylogeny and Evolution

The genus <i>Aletris</i> L. (Nartheciaceae) encompasses approximately 21-24 species distributed in East Asia and North America, yet taxonomic ambiguity persists due to overlapping morphological traits among closely related species. During fieldwork in southeastern Xizang, China, a morphologically distinct candidate species, <i>Aletris medogensis</i>, was discovered. To validate its taxonomic status and explore evolutionary relationships within East Asian <i>Aletris</i>, we integrated detailed morphological observation with comparative chloroplast phylogenomics. The newly proposed species is characterized by creeping stolons, narrow leaves, and glandular-pubescent inflorescences. Comparative analysis of 14 East Asian <i>Aletris</i> complete chloroplast genomes revealed a conserved quadripartite structure with species-specific variations, including pseudogenization of <i>ycf1</i>, loss of <i>rrn4.5</i>, and shifts in IR boundaries. Phylogenomic analyses strongly supported <i>A. medogensis</i> as a distinct species closely related to <i>A. alpestris</i>. We identified 18 hypervariable regions as potential molecular markers and detected signals of positive selection in genes <i>ccsA</i>, <i>cemA</i>, and <i>rps12</i>, suggesting adaptive evolution. This study confirms the recognition of <i>A. medogensis</i> as a new species endemic to the eastern Himalayas and demonstrates the utility of chloroplast genomics in resolving taxonomic complexity and understanding evolutionary mechanisms in <i>Aletris</i>.